Thursday, February 24, 2011

Everybody who has been aboard a ship has heard the advice: if you feel unsteady, look at the horizon. For a study published in Psychological Science, a journal of the Association for Psychological Science, researchers measured how much people sway on land and at sea and found there’s truth in that advice; people aboard a ship are steadier if they fix their eyes on the horizon.

Thomas A. Stoffregen of the University of Minnesota has been studying “body sway” for decades—how much people rock back and forth in different situations, and what this has to do with motion sickness. In just a normal situation, standing still, people move back and forth by about four centimeters every 12 to 15 seconds. Stoffregen and his coauthors, Anthony M. Mayo and Michael G. Wade, wanted to know how this changes when you’re standing on a ship.

To study posture at sea, Stoffregen made contact with the U.S. consortium that runs scientific research ships. “I’m really an oddball for these folks, because they’re studying oceanography, like hydrothermal vents. Here’s this behavioral scientist, calling them up,” he says. He boards a ship when it is travelling between different projects—for example, in this study, he rode on the research vessel Atlantis as it went between two points in the Gulf of California. “It had nothing to do with the fact that I like cruising near the tropics,” he jokes. Since the ships are between scientific expeditions, he can sleep in one of the empty bunks normally reserved for ocean scientists, and crew members volunteer to take part in his study.

The study compared the same people standing on dry land—a dock in Guaymas, Mexico—and aboard the ship. In each experiment, the crew member stood comfortably on a force plate and focused on a target—either something about 16 inches in front of them, or a far-off point; a distant mountain when standing on land or the horizon when standing on the ship. On land, people were steadier when they looked at the close-up target and swayed more when they looked far away. On the ship, however, they were steadier when they looked at the horizon.

This is actually counterintuitive, Stoffregen says. When you’re standing on a ship, you need to adjust to the ship’s movement, or you’ll fall over. So why would it help to look at the horizon and orient yourself to the Earth? He thinks it may help stabilize your body by helping you differentiate between sources of movement—the natural movement coming from your body and the movement caused by the ship.

Stoffregen thinks this motion of bodies may predict motion sickness. “It’s the people who become wobbly who subsequently become motion sick,” he says. He had originally hoped to study seasickness directly, but so far his subjects have all been seasoned crew members who are used to the ship’s movement and don’t get sick; his dream is to do his experiments aboard a ship full of undergraduate oceanography majors going to sea for the first time. “I’d give my right arm to get on one of those.”

For the first time, scientists have mapped the genome--the genetic code--of orangutans. This new tool may be used to support efforts to maintain the genetic diversity of captive and wild orangutans. The new map of the orangutan genome may also be used to help improve our understanding of the evolution of primates, including humans.

Partially funded by the National Science Foundation, the orangutan study appeared in the Jan. 27 issue of Nature. It was conducted by an international team of scientists led by Devin P. Locke of the Genome Center at Washington University.

The name "orangutan" is derived from the Malay term, "man of the forest," a fitting moniker for one of our closest relatives.

There are two species of orangutans, defined primarily by their island of origin--either Sumatra or Borneo. The outlook for orangutan survival is currently dire because there are estimated to be only about 7,500 orangutans in Sumatra, where they are considered critically endangered, and only about 50,000 orangutans in Borneo, where they are considered endangered.

The endangerment status of orangutans is determined by the International Union for Conservation of Nature.

There are no other wild populations of orangutans other than those in Sumatra and Borneo. The decline of the Sumatran and Borneo populations of orangutans is caused by varied threats, such as illegal logging, the conversion of rain forests to farmland and palm oil plantations, hunting and diseases.

Using a mix of legacy and novel technologies, the research team mapped the genomes of a total of 11 orangutans, including representatives of both the Sumatran and Bornean species.

The map of the orangutan genome may support conservation efforts by helping zoos create breeding programs designed to maintain the genetic diversity of captive populations. (The greater the genetic diversity of a species, the more resilient it is against threats to its survival.) The genome map may also help conservationists sample the genetic diversity of wild populations so they can prioritize populations of wild orangutans for conservation efforts.

After scientists map a species' genome, they compare it to the genetic maps of other species. As they do so, they search for key differences that involve duplications, deletions and inversions of genetic material. These differences may contribute to the unique features of particular species. They may also provide information about general evolutionary trends, such as the overall rate at which genomic evolution has occurred.

Before the orangutan's genome was mapped, the genetic codes of three other great primates--humans, chimpanzees and rhesus macaques--were mapped.

The genomes of the gorilla and bonobo will soon be mapped, as well.

Analyses of the orangutan genome reveal that this primate has many unique features. For example, comparisons of the structural variation of the genomes of orangutans, humans, chimpanzees and rhesus macaques indicate that during the last 15 million years or so of primate evolution, the orangutan genome has generally been more stable than those of the other primates, with fewer large-scale structural changes.

The orangutan genome also allowed for an analysis of fast-evolving genes, which are likely to have responded to evolutionary pressure for adaptation. Genes related to visual perception and metabolic processes were found to evolve unusually rapidly in orangutans and other primates. The orangutan's metabolism-related genes were also found to have evolved rapidly--a phenomenon that may be related to the orangutan's slow growth rate, slow reproduction rate, and long inter-birth interval, the period between successive births. Orangutans give birth not more than once every six to eight years, an inter-birth interval rated as the longest among mammals, including humans.

Comparisons of the population genetics of the Sumatran and Bornean species indicate that these species split approximately 400,000 years ago, which is more recent than previously believed. In addition, Sumatran orangutans have greater genetic diversity than their Bornean counterparts, despite their smaller population size and higher endangered status.

Adam Siepel, a research team member from Cornell University described the new map of the genetic code of orangutans as an important step in genome sequencing of primates. "The orangutan genome gives us a much more complete picture of genome evolution in the great apes," he said.

"This is a terrific example of the application of genome sequencing beyond model organisms--well-studied organism like the mouse and fruit fly," said Reed Beaman, an NSF program director. "Research like this has only recently become possible through a dramatic decrease in the cost of sequencing. These results demonstrate broad significance to biogeography, genetics, as well as to conservation and human evolution, and they are only starting to scratch the surface."

Scientists have discovered that the animal with the most genes--about 31,000--is the near-microscopic freshwater crustacean Daphnia pulex, or water flea.

By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.

The water flea's genome is described in a Science paper published by members of the Daphnia Genomics Consortium, an international network of scientists led by the Center for Genomics and Bioinformatics (CGB) at Indiana University (IU) Bloomington and the U.S. Department of Energy's Joint Genome Institute.

"Daphnia's high gene number is largely because its genes are multiplying, creating copies at a higher rate than other species," said project leader and CGB genomics director John Colbourne.

"We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans."

"This analysis of the Daphnia genome significantly advances our understanding of how an organism's genome interacts with its environment both to influence genome structure and to confer ecological and evolutionary success," says Saran Twombly, program director in the National Science Foundation (NSF)'s Division of Environmental Biology, which funded the research.

"Because the ecology of Daphnia pulex is well-known, and the organism occurs abundantly in the wild, this analysis provides unprecedented insights into the feedback between genes and environment in a real and ever-changing environment."

Daphnia's genome is no ordinary genome.

What reasons might Daphnia have so many genes compared to other animals?

A possibility, Colbourne said, is that "since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."

Scientists have studied Daphnia for centuries because of its importance in aquatic food webs and for its transformational responses to environmental stress.

Like the virgin nymph of Greek mythology that shares its name, Daphnia thrives in the absence of males--by clonal reproduction, until harsh environmental conditions favor the benefits of sex.

"More than one-third of Daphnia's genes are undocumented in any other organism--in other words, they are completely new to science," says Don Gilbert, paper co-author and scientist at IU Bloomington.

Sequenced genomes often contain some fraction of genes with unknown functions, even among the most well-studied genetic model species for biomedical research, such as the fruit fly Drosophila.

By using microarrays (containing millions of DNA strands affixed to microscope slides), experiments that subjected Daphnia to environmental stressors point to these unknown genes having ecologically significant functions.

"If such large fractions of genomes evolved to cope with environmental challenges, information from traditional model species used only in laboratory studies may be insufficient to discover the roles for a considerable number of animal genes," Colbourne said.

Daphnia is emerging as a model organism for a new field of science--environmental genomics--that aims to better understand how the environment and genes interact.

This includes a practical need to apply scientific developments from this field to managing our water resources and protecting human health from chemical pollutants in the environment.

James Klaunig, a scientist at IU Bloomington, predicts that the work will yield a more realistic and scientifically-based risk evaluation.

"Genome research on the responses of animals to stress has important implications for assessing environmental risks to humans," Klaunig said. "Daphnia is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary."

"With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

The scientists learned that of all sequenced invertebrate genomes so far, Daphnia shares the most genes with humans.

Daphnia's gene expression patterns change depending on its environment, and the patterns indicate what state its cells are in.

A water flea bobbing in water containing a chemical pollutant will tune-up or tune-down a suite of genes differently than its sisters accustomed to water without the pollutant, for example.

The health effects of most industrially produced compounds in the environment are unknown, because current testing procedures are too slow, too costly, and unable to indicate the causes for their effects on animals, including humans.

Over the course of the project, the Daphnia Genomics Consortium has grown from a handful of founding members to more than 450 investigators around the globe.

"Assembling so many experts around a shared research goal is no small feat," said Peter Cherbas, director of the CGB. "The genome project signals the coming-of-age of Daphnia as a research tool for investigating the molecular underpinnings of key ecological and environmental problems."

Colbourne agreed, adding, "New model systems rarely arrive on the scene with such clear and important roles to play in advancing a new field of science."

Pigeons rely mainly on their olfactory sense when they navigate. Young pigeons learn to recognize environmental odours carried by the winds into the loft and to use these odours to find their way home from unfamiliar territory. Scientists from the Max Planck Institute for Ornithology in Radolfzell, Anna Gagliardo from the University of Pisa, and their colleagues at the University of Trient recently demonstrated that pigeons navigate more poorly with their right nostril blocked. This finding suggests that the left brain hemisphere, where olfactory information is processed, is of fundamental importance to the orientation and navigation of homing pigeons.

The amazing ability of pigeons to find their way to their home loft has been known for centuries. According to scientists, these birds possess a distinctive olfactory sense as well as a capacity for recognizing odours, which helps them to develop a kind of “scent map” of their surroundings. However, it seems that pigeons cannot smell similarly with both nostrils. Like humans, they can detect odours better through their right nostril.

Martin Wikelski from the Max Planck Institute for Ornithology in Radolfzell and Anna Gagliardo from the University of Pisa recently completed a study of 31 pigeons to determine how the birds’ orientation would be affected if the they were unable to smell through their right nostril. The scientists inserted small, rubbery, removable plugs into the left nostril of some of the birds and into the right nostril of others. All the pigeons were hand-raised in the area around of Pisa. After fixing small GPS data loggers on the pigeons’ backs, the researchers released the pigeons near Cigoli, a Tuscan village 42 km away from the birds’ home.

Based on the GPS data they collected, the scientists found that the pigeons that could not breathe through their right nostril took a more tortuous route. They stopped more often, and spent more time exploring the surroundings of the stopover sites than those birds that could smell with their right nostril. “We suppose that these birds had to stop to gather additional information about their surroundings because they could not navigate by their olfactory sense,” says Anna Gagliardo. “This behaviour not only indicates that an asymmetry exists in the perception and processing of odours between the left and the right olfactory system; it also shows that the right nostril apparently plays an important role in processing olfactory information in the left hemisphere that is useful for navigation.” How the pigeons’ brains process these sensory perceptions, and why this processing is asymmetric, the researchers do not yet know.

After a decade of experimental development, data-taking, and analysis, an international research team led by scientists from Boston University and the University of Illinois has announced a new value for the muon lifetime.

The new lifetime measurement—the most precise ever made of any subatomic particle—makes possible a new determination of the strength of the weak nuclear force. Experiments for this research were conducted using the proton accelerator facility of the Paul Scherrer Institute (PSI) in Villigen, Switzerland. The results were published in the January 25, 2011 issue of the journal Physical Review Letters.

The weak force is one of the four fundamental forces of nature. Although rarely encountered in everyday life, the weak force is at the heart of many elemental physical processes, including those responsible for making the sun shine. All four of the fundamental forces are characterized by coupling constants, which describe their strength. The famous constant G, in Newton’s law of gravitation, determines the gravitational attraction between any two massive objects. The fine structure constant determines the strength of the electrostatic force between charged particles. The coupling constant for the weak interactions, known as the Fermi constant, is also essential for calculations in the world of elementary particles. Today, physicists regard the weak and the electromagnetic interaction as two aspects of one and the same interaction. Proof of that relationship, established in the 1970s, was an important breakthrough in our understanding of the subatomic world.

The new value of the Fermi constant was determined by an extremely precise measurement of the muon lifetime. The muon is an unstable subatomic particle which decays with a lifetime of approximately two microseconds (two millionths of a second). This decay is governed by the weak force only, and the muon's lifetime has a relatively simple relationship to the strength of the weak force. "To determine the Fermi constant from the muon lifetime requires elegant and precise theory, but until 1999, the theory was not as good as the experiments," says David Hertzog, professor of physics at the University of Washington. (At the time of the experiment, Hertzog was at the University of Illinois.) “Then, several breakthroughs essentially eliminated the theoretical uncertainty. The largest uncertainty in the Fermi constant determination was now based on how well the muon lifetime had been measured."

The MuLan (Muon Lifetime Analysis) experiment used muons produced at PSI’s proton accelerator—the most powerful source of muons in the world and the only place where this kind of experiment can be done. "At the heart of the experiment were special targets that caught groups of positively charged muons during a ‘muon fill period,’" says PSI’s Bernhard Lauss. "The beam was then rapidly switched off, leaving approximately 20 muons in the target. Each muon would eventually decay, typically ejecting an energetic positron—a positively charged electron—to indicate its demise. The positrons were detected using a soccer-ball shaped array of 170 detectors, which surrounded the target." Boston University physics professor Robert Carey adds, "We repeated this procedure for 100 billion muon fills, accumulating trillions of individual decays. By the end, we had recorded more than 100 terabytes of data, far more than we could handle by ourselves. Instead, the data was stored and analyzed at the National Center for Supercomputing Applications (NCSA) in Illinois." A distribution of how long each muon lived before it decayed was created from the raw data and then fit to determine the mean lifetime: 2.1969803 ±0.0000022 microseconds. The uncertainty is approximately 2 millionths of a millionth of a second - a world record.

Synchrotron X-ray investigation of a fossilised snake with legs is helping scientists to better understand how in the course of evolution snakes have lost their legs, and whether they evolved from terrestrial lizards or from reptiles living in the oceans. New 3-D X-ray images reveal that the internal architecture of the ancient snake’s leg bones resemble those of modern terrestrial lizard legs. The results are published on 8 February in the Journal of Vertebrate Paleontology.

A novel X-ray imaging technology is helping scientists to better understand how in the course of evolution snakes have lost their legs. The researchers hope that the new data will help to resolve a heated debate about the origin of snakes: whether they evolved from a terrestrial lizard or from one that lived in the oceans. New, detailed 3-D images reveal that the internal architecture of an ancient snake’s leg bones strongly resembles those of modern terrestrial lizard legs. The results are published in the 8 February issue of the Journal of Vertebrate Paleontology.

The team of researchers was led by Alexandra Houssaye from Museum National d'Histoire Naturelle (MNHN) and CNRS in Paris, France, and included scientists from the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, where the X-ray imaging was performed, and the Karlsruhe Institute of Technology (KIT), Germany, where a sophisticated technique and a dedicated instrument to take the images were developed.

Only three specimens exist of fossilised snakes with preserved leg bones. Eupodophis descouensi, the ancient snake studied in this experiment, was discovered ten years ago in 95-million-year-old rocks in Lebanon. About 50 cm long overall, it exhibits a small leg, about 2 cm long, attached to the animal’s pelvis. This fossil is key to understanding the evolution of snakes, as it represents an intermediate evolutionary stage when ancient snakes had not yet completely lost the legs they inherited from earlier lizards. Although the fossil exhibits just one leg on its surface, a second leg was thought to be concealed in the stone, and indeed this leg was revealed in full detail thanks to synchrotron X-rays.

The high-resolution 3-D images, in particular the fine details of the buried small leg, suggest that this species lost its legs because they grew more slowly, or for a shorter period of time. The data also reveal that the hidden leg is bent at the knee and has four ankle bones but no foot or toe bones.

"The revelation of the inner structure of Eupodophis hind limbs enables us to investigate the process of limb regression in snake evolution," says Alexandra Houssaye.

The scientists used synchrotron laminography, a recent imaging technique specially developed for studying large, flat samples. It is similar to the computed tomography (CT) technique used in many hospitals, but uses a coherent synchrotron X-ray beam to resolve details a few micrometres in size — some 1000 times smaller than a hospital CT scanner. For the new technique, the fossil is rotated at a tilted angle in a brilliant high-energy X-ray beam, with thousands of two-dimensional images recorded as it makes a full 360-degree turn. From these individual images, a high-resolution, 3-D representation is reconstructed, which shows hidden details like the internal structure(s) of the legs.

"Synchrotrons, these enormous machines, allow us to see microscopic details in fossils invisible to any other techniques without damage to such invaluable specimens," says Paul Tafforeau of the ESRF, a co-author of the study.